The evolution of nitrogen fixation in cyanobacteria

Bioinformatics

Volumn 28, Issue 5, 2012, Pages 603-606

  Latysheva, Natasha ^a   Junker, Vivien L ^a   Palmer, William J ^a,b   Codd, Geoffrey A ^c   Barker, Daniel ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c Dentistry and Nursing   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYANOBACTERIA;

BACTERIAL PROTEIN; NITROGENASE;

ARTICLE; CLASSIFICATION; CYANOBACTERIUM; EVOLUTION; GENETICS; HORIZONTAL GENE TRANSFER; METABOLISM; NITROGEN FIXATION; PHYLOGENY;

BACTERIAL PROTEINS; BIOLOGICAL EVOLUTION; CYANOBACTERIA; GENE TRANSFER, HORIZONTAL; NITROGEN FIXATION; NITROGENASE; PHYLOGENY;

EID: 84857878555     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts008     Document Type: Article

References (51)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Barker,D. and Pagel,M. (2005) Predicting functional gene links from phylogeneticstatistical analyses of whole genomes. PLoS Comput. Biol., 1, e3.
3. Barker,D. et al. (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics, 23, 14-20.
4. Berman-Frank,I. et al. (2003) Nitrogen fixation and photosynthetic oxygen evolution in cyanobacteria. Res. Microbiol., 154, 157-164.
5. Blank,C.E. and Sánchez-Baracaldo,P. (2010) Timing of morphological and ecological innovations in the cyanobacteria - a key to understanding the rise in atmospheric oxygen. Geobiology, 8, 1-23.
6. Boyd,E.S. et al. (2011) A late methanogen origin for molybdenum-dependent nitrogenases. Geobiology, 9, 221-232.
7. Broda,E and Peschek,G.A. (1983) Nitrogen fixation as evidence for the reducing nature of the early biosphere, Biosystems, 16, 1-8.
8. Buschbom,J. and Barker,D. (2006) Evolutionary history of vegetative reproduction in Porpidia s.l. (lichen-forming Ascomycota). Syst. Biol., 55, 471-484.
9. Catling,D.C. et al. (2001) Biogenic methane, hydrogen escape, and the irreversible oxidation of early Earth. Science, 293, 839-843.
10. Codd,G.A. et al. (2005) Cyanobacterial toxins: risk management for health protection. Toxicol. Appl. Pharm., 203, 264-272.
11. Criscuolo,A and Gribaldo,S. (2011) Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria. Mol. Biol. Evol., 28, 3019-3032.
12. David,L.A. and Alm,E.J. (2011) Rapid evolutionary innovation during an Archaean genetic expansion. Nature, 469, 93-96.
13. Fani,R. et al. (2000) Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes. J. Mol. Evol., 51, 1-11.
14. Felsenstein,J. (1988) Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet., 22, 521-565.
15. Gupta,R.S. (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int. J. Syst. Evol. Microbiol., 59, 2510-2526.
16. Henson,B.J. et al. (2004) Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD. Int. J. Syst. Evol. Micr., 54, 493-497.
17. Hu,Q. et al. (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J., 54, 621-639.
18. Huelsenbeck,J.P. et al. (2003) Stochastic mapping of morphological characters. Syst. Biol., 52, 131-158.
19. Irisarri,P. et al. (2001) Cyanobacteria in Uruguayan rice fields: diversity, nitrogen fixing ability and tolerance to herbicides and combined nitrogen. J. Biotechnol., 91, 95-103.
20. Iturriaga,R. and Mitchell,B.G. (1986) Chroococcoid cyanobacteria: a significant component in the food web dynamics of the open ocean. Mar. Ecol. Prog. Ser., 28, 291-297.
21. Kasting,J.F. and Siefert,J.L. (2001) Biogeochemistry: the nitrogen fix. Nature, 412, 26-27.
22. Kasting,J.F. and Siefert,J.L (2002) Life and the evolution of Earth's atmosphere. Science, 296, 1066-1068.
23. Larsson,J. et al. (2011) Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits. BMC Evol. Biol., 11, 187.
24. Leigh,J.A. (2000) Nitrogen fixation in Methanogens: an Archaeal perspective. Curr. Issues Mol. Biol., 2, 125-131.
25. Li,L. et al. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
26. Lutzoni,F. et al. (2001) Major fungal lineages are derived from lichen symbiotic ancestors. Nature, 411, 937-940.
27. Lyons,E.M. and Thiel,T. (1995). Characterization of nifB, nifS, and nifU genes in the cyanobacterium Anabaena variabilis: nifB is required for the vanadium-dependent nitrogenase. J. Bacteriol., 177, 1570-1575.
28. Mehta,M.P. and Baross,J.A. (2006) Nitrogen fixation at 92°C by a hydrothermal vent archaeon. Science, 314, 1783-1786.
29. Navarro-González,R. et al. (2001) A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning. Nature, 412, 61-64.
30. Nielsen,R. (2002) Mapping mutations on phylogenies. Syst. Biol., 51, 729-739.
31. Noffke,N. et al. (2008) An actualistic perspective into Archean worlds - (cyano-) bacterially induced sedimentary structures in the siliciclastic Nhlazatse Section, 2.9 Ga Pongola Supergroup, South Africa. Geobiology, 6, 5-20.
32. Normand,P. et al. (1992) Nucleotide sequence of nifD from Frankia alni strain Ar13: phylogenetic inferences. Mol. Biol. Evol., 9, 495-506.
33. Olson,J.M. (2006) Photosynthesis in the Archean era. Photosyn. Res., 88, 109-117.
34. Paerl,H.W. (2000) Marine plankton. In Whitton,B.A. and Potts,M. (eds) The Ecology of Cyanobacteria. Kluwer Academic Publishers, Netherlands, pp. 121-148.
35. Pagel,M. (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol., 48, 612-622.
36. Postgate,J.R. and Eady,R.R. (1988) The evolution of biological nitrogen fixation. In Bother,H. et al. (eds) Nitrogen Fixation: Hundred Years After. Proceedings of the 7th International Congress on Nitrogen Fixation. Gustav Fischer, Stuttgart, pp. 31-40.
37. Raven,J.A. and Yin,Z.H. (1998) The past, present and future of nitrogenous compounds in the atmosphere, and their interactions with plants. New Phytol., 139, 205-219.
38. Raymond,J. et al. (2004) The natural history of nitrogen fixation. Mol. Biol. Evol., 21, 541-554.
39. Ruvkun,G.B. and Ausubel,F.M. (1980) Interspecies homology of nitrogenase genes. Proc. Natl Acad. Sci. USA 77, 191-195.
40. Sánchez-Baracaldo,P. et al. (2005) Morphological and habitat evolution in the cyanobacteria using a compartmentalization approach. Geobiology, 3, 145-165.
41. Scherer,S. et al. (1988) Interaction of photosynthesis, respiration and nitrogen fixation in cyanobacteria. Photosynth. Res., 15, 95-114.
42. Shi,T. and Falkowski,P.G. (2008) Genome evolution in cyanobacteria: The stable core and the variable shell. Proc. Natl Acad. Sci. USA, 105, 2510-2515.
43. Stucken,K. et al. (2010) The smallest known genomes of multicellular and toxic cyanobacteria: comparison, minimal gene sets for linked traits and the evolutionary implications. PLoS ONE, 5, e9235.
44. Swingley,W.D. et al. (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol. Biol. Evol., 25, 643-654.
45. Tomitani,A. et al. (2006) The evolutionary diversification of cyanobacteria: Molecularphylogenetic and paleontological perspectives. Proc. Natl Acad. Sci. USA, 103, 5442-5447.
46. Towe,K.M. (2002) Evolution of nitrogen fixation. Science, 295, 798-799.
47. Van Dongen,S. (2000) A Cluster Algorithm for Graphs. Technical Report INSR0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam.
48. Vitousek,P.M. et al. (2002) Towards an ecological understanding of biological nitrogen fixation. Biogeochemistry, 57-58, 1-45.
49. Yang,Z. (2006) Computational Molecular Evolution. Oxford University Press, Oxford.
50. Young,J.P.W. (1992). Phylogenetic classification of nitrogen-fixing organisms. In Stacey,G. et al. (eds) Biological Nitrogen Fixation. Chapman & Hall, New York, pp. 43-86.
51. Zehr,J.P. et al. (1997) Phylogeny of cyanobacterial nifH genes: evolutionary implications and potential applications to natural assemblages. Microbiology, 143, 1443-1450.